Multiple sequence alignment - TraesCS3B01G176200
Loading Multiple Alignment...
BLAST Results
BLAST Results - Input Sequence
Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
to extract flanking regions for cloning. If the result of the multiple sequence alignment is
not as expected, these results could be used for further investigation.
qseqid
sseqid
percentage.identical
alignment.length
no.mismatch
no.gap.openings
qstart
qend
sstart
send
evalue
bitscore
0
TraesCS3B01G176200
chr3B
100.000
3056
0
0
1
3056
178926738
178929793
0.000000e+00
5644
1
TraesCS3B01G176200
chr3D
91.850
3092
145
62
3
3056
124864660
124867682
0.000000e+00
4215
2
TraesCS3B01G176200
chr3A
92.877
2822
124
34
1
2785
132580431
132583212
0.000000e+00
4026
3
TraesCS3B01G176200
chr3A
83.333
294
23
11
2782
3056
132583247
132583533
6.540000e-62
248
BLAST Results - HSPs grouped
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
purely upstream or downstream may be removed if they don't overlap both primers.
query
scaffold
start
end
length
rev.comp
avg.bitscore
max.bitscore
avg.percent.identical
query.start
query.end
num_hsp
groupid
homo_length
0
TraesCS3B01G176200
chr3B
178926738
178929793
3055
False
5644
5644
100.000
1
3056
1
chr3B.!!$F1
3055
1
TraesCS3B01G176200
chr3D
124864660
124867682
3022
False
4215
4215
91.850
3
3056
1
chr3D.!!$F1
3053
2
TraesCS3B01G176200
chr3A
132580431
132583533
3102
False
2137
4026
88.105
1
3056
2
chr3A.!!$F1
3055
AutoCloner calculated primer pairs
These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
whilst remaining within the specified product range where possible.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
543
561
0.033504
GTGACACGAAAGGCAGGAGA
59.966
55.0
0.0
0.0
0.0
3.71
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2210
2246
0.107165
CCCTCTTCCGGGGATTGTTC
60.107
60.0
0.0
0.0
46.5
3.18
R
All possible primers
Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
during PCR or sequencing,
these could be used as alternatives.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
30
31
8.166726
ACATCACCCTTTTTCTAAGAATTCTCT
58.833
33.333
8.78
2.11
0.00
3.10
31
32
8.672815
CATCACCCTTTTTCTAAGAATTCTCTC
58.327
37.037
8.78
0.00
0.00
3.20
91
102
0.894141
GTAAACATGGTGGGCATGCA
59.106
50.000
21.36
0.00
33.61
3.96
126
137
6.610075
ATGATTTGAGCACAATTAAACCCT
57.390
33.333
0.00
0.00
35.85
4.34
209
221
4.662961
TGGCCGCGTGACAGAGTG
62.663
66.667
4.92
0.00
0.00
3.51
493
505
0.895559
AAAAAGCGGCAGAAGGGAGG
60.896
55.000
1.45
0.00
0.00
4.30
494
506
2.771328
AAAAGCGGCAGAAGGGAGGG
62.771
60.000
1.45
0.00
0.00
4.30
543
561
0.033504
GTGACACGAAAGGCAGGAGA
59.966
55.000
0.00
0.00
0.00
3.71
545
563
0.603569
GACACGAAAGGCAGGAGAGA
59.396
55.000
0.00
0.00
0.00
3.10
658
677
2.515979
TGTTCCGAGCCAGGAGCAA
61.516
57.895
11.26
0.00
46.21
3.91
740
759
3.747852
ACTCCATTCCCCATTCCTTCTA
58.252
45.455
0.00
0.00
0.00
2.10
754
779
1.132500
CTTCTACATCACCCTCCCCC
58.868
60.000
0.00
0.00
0.00
5.40
791
816
0.908198
ATCTCAACAGCACCTCCCTC
59.092
55.000
0.00
0.00
0.00
4.30
803
828
2.123251
TCCCTCATCGCCTCCTCC
60.123
66.667
0.00
0.00
0.00
4.30
848
877
1.378762
CTTTTCGCCTTCCCCTCCA
59.621
57.895
0.00
0.00
0.00
3.86
850
879
2.420466
TTTTCGCCTTCCCCTCCACC
62.420
60.000
0.00
0.00
0.00
4.61
912
942
1.657556
GCCTGCCTTGCGTTTTACA
59.342
52.632
0.00
0.00
0.00
2.41
985
1015
3.244112
CGAGTGGAGTTTTAGGGTGAGTT
60.244
47.826
0.00
0.00
0.00
3.01
1017
1047
1.614711
GATGTGGCCCATGGAGGAA
59.385
57.895
15.22
0.00
41.22
3.36
1062
1092
2.126424
GAGCACGTCGAGGTGACC
60.126
66.667
35.27
23.05
45.23
4.02
1100
1130
4.448976
GGCCAAGGGGAAGGAGGC
62.449
72.222
0.00
0.00
44.48
4.70
1146
1176
1.296715
GGTGAGGGTGTTCTGCGAT
59.703
57.895
0.00
0.00
0.00
4.58
1149
1179
0.904649
TGAGGGTGTTCTGCGATGAT
59.095
50.000
0.00
0.00
0.00
2.45
1170
1200
2.582498
GACGCCACCGATTCCTCG
60.582
66.667
0.00
0.00
44.62
4.63
1710
1740
0.907230
GCTCCTTCCCTCAGTCCACT
60.907
60.000
0.00
0.00
0.00
4.00
1715
1745
1.194781
TTCCCTCAGTCCACTCTGGC
61.195
60.000
0.00
0.00
37.47
4.85
1768
1798
2.197605
TCGTCGTCTTCCAGCACCA
61.198
57.895
0.00
0.00
0.00
4.17
2004
2034
2.357517
CAGCAGGCGGACGAGTTT
60.358
61.111
0.00
0.00
0.00
2.66
2057
2087
2.565645
CCCTCCCCGTCATCTAGCG
61.566
68.421
0.00
0.00
0.00
4.26
2058
2088
1.528542
CCTCCCCGTCATCTAGCGA
60.529
63.158
0.00
0.00
0.00
4.93
2069
2099
4.619760
CGTCATCTAGCGAAACAACTGTAA
59.380
41.667
0.00
0.00
0.00
2.41
2070
2100
5.118050
CGTCATCTAGCGAAACAACTGTAAA
59.882
40.000
0.00
0.00
0.00
2.01
2071
2101
6.346279
CGTCATCTAGCGAAACAACTGTAAAA
60.346
38.462
0.00
0.00
0.00
1.52
2072
2102
6.790825
GTCATCTAGCGAAACAACTGTAAAAC
59.209
38.462
0.00
0.00
0.00
2.43
2122
2152
6.291849
CGGTCAAATTTTGTTTGCATTCGTTA
60.292
34.615
8.89
0.00
0.00
3.18
2123
2153
7.568497
CGGTCAAATTTTGTTTGCATTCGTTAT
60.568
33.333
8.89
0.00
0.00
1.89
2124
2154
8.067189
GGTCAAATTTTGTTTGCATTCGTTATT
58.933
29.630
8.89
0.00
0.00
1.40
2125
2155
9.432077
GTCAAATTTTGTTTGCATTCGTTATTT
57.568
25.926
8.89
0.00
0.00
1.40
2126
2156
9.994432
TCAAATTTTGTTTGCATTCGTTATTTT
57.006
22.222
8.89
0.00
0.00
1.82
2164
2200
9.757227
TTTCTTTTTGTCTTTCTAGAGAGAGAG
57.243
33.333
13.05
7.08
36.18
3.20
2183
2219
8.103305
AGAGAGAGGAGAGAGTATGATGTTATC
58.897
40.741
0.00
0.00
0.00
1.75
2184
2220
6.878923
AGAGAGGAGAGAGTATGATGTTATCG
59.121
42.308
0.00
0.00
0.00
2.92
2424
2465
3.045601
TGAAAAGGCGAAGAGGAGAAG
57.954
47.619
0.00
0.00
0.00
2.85
2425
2466
2.632996
TGAAAAGGCGAAGAGGAGAAGA
59.367
45.455
0.00
0.00
0.00
2.87
2426
2467
3.258228
GAAAAGGCGAAGAGGAGAAGAG
58.742
50.000
0.00
0.00
0.00
2.85
2431
2472
1.001815
GCGAAGAGGAGAAGAGGATCG
60.002
57.143
0.00
0.00
42.67
3.69
2526
2569
1.573829
GGCTGGCAATGAAACGACGA
61.574
55.000
0.00
0.00
0.00
4.20
2561
2604
3.864686
CCGGCGATGTTTGGAGCG
61.865
66.667
9.30
0.00
0.00
5.03
2694
2747
6.878389
CACCCCAACATTAACTGCATTATTTT
59.122
34.615
0.00
0.00
0.00
1.82
2712
2765
1.523154
TTCGGAAATTTGCTGGCGCT
61.523
50.000
7.64
0.00
36.97
5.92
2795
2855
5.006746
GGATTTGCTGGTACGAGATTAGTTG
59.993
44.000
9.33
0.00
0.00
3.16
2796
2856
3.520290
TGCTGGTACGAGATTAGTTGG
57.480
47.619
9.33
0.00
0.00
3.77
2797
2857
2.202566
GCTGGTACGAGATTAGTTGGC
58.797
52.381
9.33
0.00
0.00
4.52
2825
2926
2.093447
CCGAGTCTTGGGCTGTAAGAAT
60.093
50.000
0.00
0.00
36.06
2.40
2923
3025
1.374947
CTGACAAAAGGGAGCGGGA
59.625
57.895
0.00
0.00
0.00
5.14
2936
3038
2.093128
GGAGCGGGAGATTAGGAAAACA
60.093
50.000
0.00
0.00
0.00
2.83
2947
3062
4.584327
TTAGGAAAACAAAAGCTGGCTC
57.416
40.909
0.00
0.00
0.00
4.70
2948
3063
1.338020
AGGAAAACAAAAGCTGGCTCG
59.662
47.619
0.00
0.00
0.00
5.03
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
10
11
9.513906
AAGAAGAGAGAATTCTTAGAAAAAGGG
57.486
33.333
9.87
0.00
43.44
3.95
45
46
5.315109
GGGGGTAAATTGGGGAGTATCTTAT
59.685
44.000
0.00
0.00
33.73
1.73
55
56
1.310877
TACCTGGGGGTAAATTGGGG
58.689
55.000
0.00
0.00
45.32
4.96
91
102
1.281867
TCAAATCATTCCTGGCGACCT
59.718
47.619
0.00
0.00
0.00
3.85
209
221
3.645212
GTCAGGGTAGTAAAGGGTATCCC
59.355
52.174
0.00
0.00
45.90
3.85
426
438
5.563842
GCGAATCTGAATCGATTTTTCACT
58.436
37.500
18.52
0.00
42.76
3.41
511
523
1.774217
TGTCACCTTTCCTGCCCCT
60.774
57.895
0.00
0.00
0.00
4.79
543
561
7.233553
CCCCTGTTTTCTTCCTTTTCTATTTCT
59.766
37.037
0.00
0.00
0.00
2.52
545
563
6.270000
CCCCCTGTTTTCTTCCTTTTCTATTT
59.730
38.462
0.00
0.00
0.00
1.40
658
677
2.830285
GCGGCGTCCTGTTGTTTGT
61.830
57.895
9.37
0.00
0.00
2.83
706
725
2.817396
GGAGTTGCTGCTCTCGCC
60.817
66.667
15.05
7.48
35.89
5.54
754
779
2.438795
TTTTTGGGGGCGGAGAGG
59.561
61.111
0.00
0.00
0.00
3.69
791
816
3.237741
GGAGGGGAGGAGGCGATG
61.238
72.222
0.00
0.00
0.00
3.84
904
934
3.689649
CCCTCAAGAATCCCTGTAAAACG
59.310
47.826
0.00
0.00
0.00
3.60
912
942
3.269643
CCTAAAACCCCTCAAGAATCCCT
59.730
47.826
0.00
0.00
0.00
4.20
985
1015
2.556622
GCCACATCGAGGAAAGGAAAAA
59.443
45.455
3.06
0.00
0.00
1.94
1017
1047
2.270352
TCACCGCCATGAAAAACTCT
57.730
45.000
0.00
0.00
0.00
3.24
1088
1118
2.757077
CAAACGCCTCCTTCCCCT
59.243
61.111
0.00
0.00
0.00
4.79
1093
1123
2.597510
GCCACCAAACGCCTCCTT
60.598
61.111
0.00
0.00
0.00
3.36
1100
1130
4.072088
GCTCGACGCCACCAAACG
62.072
66.667
0.00
0.00
0.00
3.60
1146
1176
0.390603
AATCGGTGGCGTCGAAATCA
60.391
50.000
0.00
0.00
40.15
2.57
1149
1179
1.738830
GGAATCGGTGGCGTCGAAA
60.739
57.895
0.00
0.00
40.15
3.46
1170
1200
2.866726
GCCCTCCTCCTCATCGCTC
61.867
68.421
0.00
0.00
0.00
5.03
1326
1356
1.681486
CCTCGGCCTTCCTCTTCCTC
61.681
65.000
0.00
0.00
0.00
3.71
1383
1413
1.606885
CGGCGTACTTACCCCAAGGA
61.607
60.000
0.00
0.00
38.70
3.36
1386
1416
2.265424
GCGGCGTACTTACCCCAA
59.735
61.111
9.37
0.00
0.00
4.12
1443
1473
2.485795
GGCGGTGTCAAAAGTGCCA
61.486
57.895
0.00
0.00
42.03
4.92
1449
1479
1.301401
CTCCTCGGCGGTGTCAAAA
60.301
57.895
7.21
0.00
0.00
2.44
1671
1701
1.305046
GAGGACAGAGGTCGGGGAA
60.305
63.158
0.00
0.00
45.28
3.97
1680
1710
1.671901
GGAAGGAGCGGAGGACAGAG
61.672
65.000
0.00
0.00
0.00
3.35
1683
1713
2.683933
GGGAAGGAGCGGAGGACA
60.684
66.667
0.00
0.00
0.00
4.02
1725
1755
3.966026
CTTGGAGGCGTCGTCGTCC
62.966
68.421
16.44
16.44
43.20
4.79
1735
1765
2.815647
CGACGGCTTCTTGGAGGC
60.816
66.667
0.00
0.00
38.73
4.70
1924
1954
4.606071
GCAGTCGCTGGAGAATGT
57.394
55.556
8.57
0.00
38.35
2.71
1946
1976
2.918802
ACGGGTTGTAGGCCGACA
60.919
61.111
15.44
15.44
0.00
4.35
2004
2034
5.068234
ACAAGTCGGTGATATCTTCGAAA
57.932
39.130
17.73
0.00
33.33
3.46
2010
2040
6.036083
CGATTTGAAACAAGTCGGTGATATCT
59.964
38.462
17.13
0.00
0.00
1.98
2013
2043
5.231702
TCGATTTGAAACAAGTCGGTGATA
58.768
37.500
21.82
6.60
33.46
2.15
2057
2087
5.857517
TCGGTGTTTGTTTTACAGTTGTTTC
59.142
36.000
0.00
0.00
0.00
2.78
2058
2088
5.770417
TCGGTGTTTGTTTTACAGTTGTTT
58.230
33.333
0.00
0.00
0.00
2.83
2069
2099
2.606065
GCGCCTAATTCGGTGTTTGTTT
60.606
45.455
10.89
0.00
36.91
2.83
2070
2100
1.068816
GCGCCTAATTCGGTGTTTGTT
60.069
47.619
10.89
0.00
36.91
2.83
2071
2101
0.519961
GCGCCTAATTCGGTGTTTGT
59.480
50.000
10.89
0.00
36.91
2.83
2072
2102
0.179174
GGCGCCTAATTCGGTGTTTG
60.179
55.000
22.15
0.00
36.91
2.93
2147
2177
6.127026
ACTCTCTCCTCTCTCTCTAGAAAGAC
60.127
46.154
0.00
0.00
0.00
3.01
2164
2200
6.081049
CGAACGATAACATCATACTCTCTCC
58.919
44.000
0.00
0.00
0.00
3.71
2183
2219
2.730672
GCAGCTACACAGGCGAACG
61.731
63.158
0.00
0.00
34.52
3.95
2184
2220
2.391389
GGCAGCTACACAGGCGAAC
61.391
63.158
0.00
0.00
34.52
3.95
2210
2246
0.107165
CCCTCTTCCGGGGATTGTTC
60.107
60.000
0.00
0.00
46.50
3.18
2402
2441
3.703001
TCTCCTCTTCGCCTTTTCATT
57.297
42.857
0.00
0.00
0.00
2.57
2404
2443
2.632996
TCTTCTCCTCTTCGCCTTTTCA
59.367
45.455
0.00
0.00
0.00
2.69
2405
2444
3.258228
CTCTTCTCCTCTTCGCCTTTTC
58.742
50.000
0.00
0.00
0.00
2.29
2424
2465
4.081917
ACTCTTCTGTCTTTTCCGATCCTC
60.082
45.833
0.00
0.00
0.00
3.71
2425
2466
3.835395
ACTCTTCTGTCTTTTCCGATCCT
59.165
43.478
0.00
0.00
0.00
3.24
2426
2467
3.929610
CACTCTTCTGTCTTTTCCGATCC
59.070
47.826
0.00
0.00
0.00
3.36
2431
2472
8.035394
TGATACATACACTCTTCTGTCTTTTCC
58.965
37.037
0.00
0.00
0.00
3.13
2467
2508
0.238289
CGGTCCAACGTACGTACTGT
59.762
55.000
23.12
18.14
0.00
3.55
2468
2509
0.238289
ACGGTCCAACGTACGTACTG
59.762
55.000
23.12
22.07
46.58
2.74
2469
2510
1.803334
TACGGTCCAACGTACGTACT
58.197
50.000
23.12
3.61
46.58
2.73
2503
2546
2.283101
TTTCATTGCCAGCCCGCT
60.283
55.556
0.00
0.00
0.00
5.52
2506
2549
1.212751
GTCGTTTCATTGCCAGCCC
59.787
57.895
0.00
0.00
0.00
5.19
2507
2550
1.154225
CGTCGTTTCATTGCCAGCC
60.154
57.895
0.00
0.00
0.00
4.85
2508
2551
0.179215
CTCGTCGTTTCATTGCCAGC
60.179
55.000
0.00
0.00
0.00
4.85
2509
2552
0.179215
GCTCGTCGTTTCATTGCCAG
60.179
55.000
0.00
0.00
0.00
4.85
2510
2553
1.573829
GGCTCGTCGTTTCATTGCCA
61.574
55.000
0.00
0.00
38.79
4.92
2511
2554
1.134694
GGCTCGTCGTTTCATTGCC
59.865
57.895
0.00
0.00
0.00
4.52
2512
2555
1.134694
GGGCTCGTCGTTTCATTGC
59.865
57.895
0.00
0.00
0.00
3.56
2513
2556
1.419922
CGGGCTCGTCGTTTCATTG
59.580
57.895
0.00
0.00
0.00
2.82
2694
2747
2.566010
GCGCCAGCAAATTTCCGA
59.434
55.556
0.00
0.00
44.35
4.55
2727
2780
2.489938
AGGCAAGGTAAATCTCGCAA
57.510
45.000
0.00
0.00
0.00
4.85
2759
2812
7.148820
CGTACCAGCAAATCCAACTTAATTTTG
60.149
37.037
0.00
0.00
0.00
2.44
2795
2855
0.875059
CCAAGACTCGGAAAGTTGCC
59.125
55.000
0.00
0.00
38.74
4.52
2796
2856
0.875059
CCCAAGACTCGGAAAGTTGC
59.125
55.000
0.00
0.00
38.74
4.17
2797
2857
0.875059
GCCCAAGACTCGGAAAGTTG
59.125
55.000
0.00
0.00
38.74
3.16
2923
3025
4.835056
AGCCAGCTTTTGTTTTCCTAATCT
59.165
37.500
0.00
0.00
0.00
2.40
2936
3038
3.146828
AACCCCCGAGCCAGCTTTT
62.147
57.895
0.00
0.00
0.00
2.27
2947
3062
0.039888
CGCAAGTTTAACAACCCCCG
60.040
55.000
0.00
0.00
32.70
5.73
2948
3063
0.319211
GCGCAAGTTTAACAACCCCC
60.319
55.000
0.30
0.00
41.68
5.40
3033
3148
3.699894
CCCACCAGTCGCTCTGCT
61.700
66.667
2.64
0.00
42.38
4.24
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.